BioC 3.4: CHECK report for BiocGenerics on moscato1

Package: BiocGenerics

Version: 0.19.2

Command: rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.19.2.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.19.2.tar.gz

StartedAt: 2016-09-20 04:39:50 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:41:38 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 108.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocGenerics.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && mkdir BiocGenerics.buildbin-libdir BiocGenerics.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocGenerics.buildbin-libdir BiocGenerics_0.19.2.tar.gz >BiocGenerics.Rcheck\00install.out 2>&1 && cp BiocGenerics.Rcheck\00install.out BiocGenerics-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=BiocGenerics.buildbin-libdir --install="check:BiocGenerics-install.out" --force-multiarch --no-vignettes --timings BiocGenerics_0.19.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.19.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BiocGenerics' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'utils' 'graphics' 'stats' 'parallel'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'RUnit' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'sets.Rd':
  '[GenomicRanges]{union,GRanges,GRanges-method}'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'rep':
  'rep.int'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
testPackage 6.99   0.01    7.00
plotMA      5.25   0.05    5.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'run_unitTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'run_unitTests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BiocGenerics' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'append' in package 'BiocGenerics'
Creating a new generic function for 'as.data.frame' in package 'BiocGenerics'
Creating a new generic function for 'cbind' in package 'BiocGenerics'
Creating a new generic function for 'rbind' in package 'BiocGenerics'
Creating a new generic function for 'do.call' in package 'BiocGenerics'
Creating a new generic function for 'duplicated' in package 'BiocGenerics'
Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics'
Creating a new generic function for 'eval' in package 'BiocGenerics'
Creating a new generic function for 'pmax' in package 'BiocGenerics'
Creating a new generic function for 'pmin' in package 'BiocGenerics'
Creating a new generic function for 'pmax.int' in package 'BiocGenerics'
Creating a new generic function for 'pmin.int' in package 'BiocGenerics'
Creating a new generic function for 'Reduce' in package 'BiocGenerics'
Creating a new generic function for 'Filter' in package 'BiocGenerics'
Creating a new generic function for 'Find' in package 'BiocGenerics'
Creating a new generic function for 'Map' in package 'BiocGenerics'
Creating a new generic function for 'Position' in package 'BiocGenerics'
Creating a new generic function for 'get' in package 'BiocGenerics'
Creating a new generic function for 'mget' in package 'BiocGenerics'
Creating a new generic function for 'grep' in package 'BiocGenerics'
Creating a new generic function for 'grepl' in package 'BiocGenerics'
Creating a new generic function for 'is.unsorted' in package 'BiocGenerics'
Creating a new generic function for 'lapply' in package 'BiocGenerics'
Creating a new generic function for 'sapply' in package 'BiocGenerics'
Creating a new generic function for 'lengths' in package 'BiocGenerics'
Creating a new generic function for 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'match' in package 'BiocGenerics'
Creating a new generic function for 'order' in package 'BiocGenerics'
Creating a new generic function for 'paste' in package 'BiocGenerics'
Creating a new generic function for 'rank' in package 'BiocGenerics'
Creating a new generic function for 'rownames' in package 'BiocGenerics'
Creating a new generic function for 'colnames' in package 'BiocGenerics'
Creating a new generic function for 'union' in package 'BiocGenerics'
Creating a new generic function for 'intersect' in package 'BiocGenerics'
Creating a new generic function for 'setdiff' in package 'BiocGenerics'
Creating a new generic function for 'sort' in package 'BiocGenerics'
Creating a new generic function for 'table' in package 'BiocGenerics'
Creating a new generic function for 'tapply' in package 'BiocGenerics'
Creating a new generic function for 'unique' in package 'BiocGenerics'
Creating a new generic function for 'unsplit' in package 'BiocGenerics'
Creating a new generic function for 'which' in package 'BiocGenerics'
Creating a new generic function for 'which.max' in package 'BiocGenerics'
Creating a new generic function for 'which.min' in package 'BiocGenerics'
Creating a new generic function for 'IQR' in package 'BiocGenerics'
Creating a new generic function for 'mad' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
Creating a new generic function for 'clusterCall' in package 'BiocGenerics'
Creating a new generic function for 'clusterApply' in package 'BiocGenerics'
Creating a new generic function for 'clusterApplyLB' in package 'BiocGenerics'
Creating a new generic function for 'clusterEvalQ' in package 'BiocGenerics'
Creating a new generic function for 'clusterExport' in package 'BiocGenerics'
Creating a new generic function for 'clusterMap' in package 'BiocGenerics'
Creating a new generic function for 'parLapply' in package 'BiocGenerics'
Creating a new generic function for 'parSapply' in package 'BiocGenerics'
Creating a new generic function for 'parApply' in package 'BiocGenerics'
Creating a new generic function for 'parRapply' in package 'BiocGenerics'
Creating a new generic function for 'parCapply' in package 'BiocGenerics'
Creating a new generic function for 'parLapplyLB' in package 'BiocGenerics'
Creating a new generic function for 'parSapplyLB' in package 'BiocGenerics'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'BiocGenerics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocGenerics' as BiocGenerics_0.19.2.zip
* DONE (BiocGenerics)

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.02	0.00	0.01
IQR	0	0	0
annotation	0.21	0.00	0.20
append	0	0	0
as.data.frame	0	0	0
as.vector	0.02	0.00	0.01
boxplot	0	0	0
cbind	0	0	0
clusterApply	0.01	0.00	0.02
combine	0.10	0.00	0.09
dbconn	1.74	0.01	1.77
density	0	0	0
do.call	0	0	0
duplicated	0	0	0
eval	0	0	0
evalq	0.01	0.00	0.02
fileName	1.91	0.10	2.06
funprog	0	0	0
get	0	0	0
grep	0.02	0.00	0.02
image	0	0	0
is.unsorted	0	0	0
lapply	0	0	0
lengths	0.05	0.00	0.04
mad	0	0	0
mapply	0	0	0
match	0.01	0.00	0.02
normalize	0.02	0.00	0.02
nrow	0	0	0
order	0	0	0
organism_species	0.25	0.01	0.27
paste	0	0	0
plotMA	4.77	0.05	4.90
plotPCA	2.75	0.00	2.75
rank	0.01	0.00	0.01
relist	0	0	0
rep	0	0	0
residuals	0	0	0
row_colnames	0	0	0
score	0.08	0.01	0.09
sets	0.01	0.00	0.02
sort	0	0	0
start	0.06	0.00	0.06
strand	0.10	0.02	0.11
subset	0.01	0.00	0.01
table	0.02	0.00	0.02
tapply	0	0	0
testPackage	4.94	0.00	4.94
unique	0	0	0
unlist	0	0	0
unsplit	0.02	0.00	0.02
updateObject	0.17	0.00	0.17
weights	0	0	0
which	0	0	0
xtabs	0.02	0.00	0.02

name	user	system	elapsed
BiocGenerics-package	0	0	0
Extremes	0.02	0.00	0.02
IQR	0	0	0
annotation	0.20	0.02	0.21
append	0	0	0
as.data.frame	0	0	0
as.vector	0	0	0
boxplot	0	0	0
cbind	0.02	0.00	0.01
clusterApply	0.02	0.00	0.02
combine	0.06	0.00	0.06
dbconn	1.92	0.04	1.97
density	0	0	0
do.call	0	0	0
duplicated	0	0	0
eval	0	0	0
evalq	0	0	0
fileName	2.29	0.05	2.37
funprog	0.02	0.00	0.01
get	0	0	0
grep	0	0	0
image	0	0	0
is.unsorted	0.01	0.00	0.02
lapply	0	0	0
lengths	0.05	0.00	0.05
mad	0	0	0
mapply	0	0	0
match	0	0	0
normalize	0.03	0.00	0.03
nrow	0	0	0
order	0.02	0.00	0.02
organism_species	0.28	0.01	0.29
paste	0	0	0
plotMA	5.25	0.05	5.31
plotPCA	2.89	0.00	2.88
rank	0	0	0
relist	0.02	0.00	0.02
rep	0	0	0
residuals	0	0	0
row_colnames	0.01	0.00	0.02
score	0.08	0.00	0.07
sets	0.01	0.00	0.02
sort	0	0	0
start	0.06	0.00	0.07
strand	0.10	0.00	0.09
subset	0.03	0.00	0.03
table	0	0	0
tapply	0	0	0
testPackage	6.99	0.01	7.00
unique	0	0	0
unlist	0	0	0
unsplit	0	0	0
updateObject	0.2	0.0	0.2
weights	0	0	0
which	0.02	0.00	0.02
xtabs	0	0	0